Starting phenix.real_space_refine on Thu Sep 18 18:20:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d98_46670/09_2025/9d98_46670.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d98_46670/09_2025/9d98_46670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d98_46670/09_2025/9d98_46670.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d98_46670/09_2025/9d98_46670.map" model { file = "/net/cci-nas-00/data/ceres_data/9d98_46670/09_2025/9d98_46670.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d98_46670/09_2025/9d98_46670.cif" } resolution = 4.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 113 5.16 5 C 12049 2.51 5 N 3303 2.21 5 O 3635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19100 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2781 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 21, 'TRANS': 345} Chain breaks: 4 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 61 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2601 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 310} Chain breaks: 5 Chain: "C" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2781 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 21, 'TRANS': 345} Chain breaks: 4 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 61 Chain: "D" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1076 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 135} Chain breaks: 1 Chain: "E" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1076 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 135} Chain breaks: 1 Chain: "F" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1102 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 138} Chain breaks: 1 Chain: "G" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "H" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 800 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 98} Chain: "I" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "J" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 800 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 98} Chain: "K" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 800 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 98} Chain: "M" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "N" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "O" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "P" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.81, per 1000 atoms: 0.25 Number of scatterers: 19100 At special positions: 0 Unit cell: (108, 150.12, 151.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 113 16.00 O 3635 8.00 N 3303 7.00 C 12049 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.08 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 378 " distance=2.04 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.05 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 16 " - pdb=" SG CYS M 84 " distance=2.04 Simple disulfide: pdb=" SG CYS N 16 " - pdb=" SG CYS N 84 " distance=2.04 Simple disulfide: pdb=" SG CYS O 16 " - pdb=" SG CYS O 84 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA P 3 " - " MAN P 7 " " MAN P 4 " - " MAN P 5 " " BMA d 3 " - " MAN d 4 " ALPHA1-6 " BMA P 3 " - " MAN P 4 " " MAN P 4 " - " MAN P 6 " " BMA d 3 " - " MAN d 5 " BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " NAG-ASN " NAG P 1 " - " ASN A 88 " " NAG W 1 " - " ASN B 88 " " NAG d 1 " - " ASN C 88 " Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 789.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4508 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 40 sheets defined 19.0% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 66 through 73 Processing helix chain 'A' and resid 100 through 113 removed outlier: 3.566A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'B' and resid 99 through 117 removed outlier: 3.604A pdb=" N GLN B 103 " --> pdb=" O ASN B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 352 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 475 through 481 removed outlier: 3.645A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 74 removed outlier: 3.575A pdb=" N HIS C 72 " --> pdb=" O VAL C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.691A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU C 111 " --> pdb=" O ASP C 107 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP C 113 " --> pdb=" O ILE C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 474 through 480 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 546 removed outlier: 3.865A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 596 removed outlier: 4.295A pdb=" N GLN D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.570A pdb=" N TRP D 631 " --> pdb=" O THR D 627 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 654 removed outlier: 3.937A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU D 645 " --> pdb=" O ILE D 641 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLN D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASN D 651 " --> pdb=" O GLU D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 662 Processing helix chain 'E' and resid 523 through 527 removed outlier: 3.803A pdb=" N ALA E 526 " --> pdb=" O LEU E 523 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 523 through 527' Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 543 removed outlier: 4.064A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 596 removed outlier: 3.645A pdb=" N ARG E 579 " --> pdb=" O GLN E 575 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP E 596 " --> pdb=" O LEU E 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 626 removed outlier: 3.602A pdb=" N ASP E 624 " --> pdb=" O SER E 620 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN E 625 " --> pdb=" O GLU E 621 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 636 removed outlier: 3.654A pdb=" N TRP E 631 " --> pdb=" O THR E 627 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 654 removed outlier: 3.619A pdb=" N LEU E 645 " --> pdb=" O ILE E 641 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLN E 650 " --> pdb=" O LEU E 646 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ASN E 651 " --> pdb=" O GLU E 647 " (cutoff:3.500A) Processing helix chain 'E' and resid 657 through 662 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 537 through 542 removed outlier: 3.558A pdb=" N ALA F 541 " --> pdb=" O LEU F 537 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG F 542 " --> pdb=" O THR F 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 537 through 542' Processing helix chain 'F' and resid 573 through 596 removed outlier: 3.523A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.629A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 654 removed outlier: 3.727A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLN F 650 " --> pdb=" O LEU F 646 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ASN F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) Processing helix chain 'F' and resid 657 through 662 Processing helix chain 'G' and resid 28 through 32 removed outlier: 4.039A pdb=" N ASN G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.588A pdb=" N ASP G 86 " --> pdb=" O THR G 83 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR G 87 " --> pdb=" O SER G 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 83 through 87' Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.977A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.656A pdb=" N ASN I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.899A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.986A pdb=" N ASN K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 64 removed outlier: 3.644A pdb=" N GLN K 64 " --> pdb=" O GLN K 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 61 through 64' Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.667A pdb=" N ASP K 86 " --> pdb=" O THR K 83 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR K 87 " --> pdb=" O SER K 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 83 through 87' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.955A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 65 removed outlier: 3.533A pdb=" N TRP M 62 " --> pdb=" O ARG M 59 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP M 63 " --> pdb=" O SER M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 79 removed outlier: 3.667A pdb=" N SER M 79 " --> pdb=" O ILE M 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 58 through 65 removed outlier: 3.587A pdb=" N LEU N 61 " --> pdb=" O ARG N 58 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASP N 63 " --> pdb=" O SER N 60 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY N 65 " --> pdb=" O TRP N 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 64 removed outlier: 4.244A pdb=" N ASP O 63 " --> pdb=" O SER O 60 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 79 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 3.605A pdb=" N VAL A 38 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N CYS D 604 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AA4, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AA5, first strand: chain 'A' and resid 259 through 261 removed outlier: 5.916A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS A 445 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS A 296 " --> pdb=" O CYS A 445 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.208A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.977A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.967A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.209A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 12.892A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 359 through 361 Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.688A pdb=" N MET A 271 " --> pdb=" O GLN A 287 " (cutoff:3.500A) removed outlier: 12.892A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 11.209A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.967A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.977A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.208A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS A 296 " --> pdb=" O CYS A 445 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS A 445 " --> pdb=" O CYS A 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 457 current: chain 'A' and resid 413 through 418 Processing sheet with id=AA7, first strand: chain 'A' and resid 374 through 378 Processing sheet with id=AA8, first strand: chain 'B' and resid 83 through 86 removed outlier: 4.224A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL B 489 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LYS B 46 " --> pdb=" O VAL B 489 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ILE B 491 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL B 44 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLY B 495 " --> pdb=" O TYR B 40 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TYR B 40 " --> pdb=" O GLY B 495 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ALA B 497 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N VAL B 38 " --> pdb=" O ALA B 497 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N THR B 499 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL B 36 " --> pdb=" O THR B 499 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N VAL E 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N VAL B 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N THR E 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N TYR B 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N CYS E 604 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AB1, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.895A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 259 through 261 removed outlier: 3.834A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 10.028A pdb=" N ARG B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 11.364A pdb=" N ILE B 294 " --> pdb=" O ARG B 444 " (cutoff:3.500A) removed outlier: 9.552A pdb=" N VAL B 446 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 10.610A pdb=" N VAL B 292 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N ASN B 448 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 10.026A pdb=" N THR B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N THR B 450 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 271 through 273 removed outlier: 7.754A pdb=" N THR B 450 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 10.026A pdb=" N THR B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N ASN B 448 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 10.610A pdb=" N VAL B 292 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 9.552A pdb=" N VAL B 446 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 11.364A pdb=" N ILE B 294 " --> pdb=" O ARG B 444 " (cutoff:3.500A) removed outlier: 10.028A pdb=" N ARG B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.286A pdb=" N VAL F 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N VAL C 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N THR F 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N TYR C 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N CYS F 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.843A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AB7, first strand: chain 'C' and resid 201 through 202 Processing sheet with id=AB8, first strand: chain 'C' and resid 260 through 261 removed outlier: 6.586A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N CYS C 445 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N CYS C 296 " --> pdb=" O CYS C 445 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 12.022A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 11.986A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.758A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.351A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 11.311A pdb=" N ASP C 457 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 13.044A pdb=" N ILE C 284 " --> pdb=" O ASP C 457 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 284 through 298 current: chain 'C' and resid 359 through 361 Processing sheet with id=AB9, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.583A pdb=" N MET C 271 " --> pdb=" O GLN C 287 " (cutoff:3.500A) removed outlier: 13.044A pdb=" N ILE C 284 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 11.311A pdb=" N ASP C 457 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 11.351A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.758A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.986A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.022A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N CYS C 296 " --> pdb=" O CYS C 445 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N CYS C 445 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 443 through 457 current: chain 'C' and resid 413 through 414 Processing sheet with id=AC1, first strand: chain 'C' and resid 374 through 378 Processing sheet with id=AC2, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.463A pdb=" N LEU G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TRP G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.974A pdb=" N VAL G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.320A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AC8, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.839A pdb=" N GLU I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TRP I 50 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.839A pdb=" N GLU I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.839A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AD4, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.479A pdb=" N LEU K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TRP K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 10 through 11 removed outlier: 3.880A pdb=" N VAL K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.488A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 2 through 5 removed outlier: 6.458A pdb=" N LYS M 2 " --> pdb=" O GLN M 94 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU M 96 " --> pdb=" O LYS M 2 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL M 4 " --> pdb=" O LEU M 96 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE M 26 " --> pdb=" O GLY M 38 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLY M 38 " --> pdb=" O PHE M 26 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP M 28 " --> pdb=" O ILE M 36 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 12 through 14 Processing sheet with id=AE1, first strand: chain 'N' and resid 2 through 5 removed outlier: 6.818A pdb=" N TRP N 28 " --> pdb=" O ILE N 36 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 12 through 14 Processing sheet with id=AE3, first strand: chain 'O' and resid 2 through 5 removed outlier: 4.020A pdb=" N LYS O 2 " --> pdb=" O GLU O 92 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N PHE O 26 " --> pdb=" O GLY O 38 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLY O 38 " --> pdb=" O PHE O 26 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP O 28 " --> pdb=" O ILE O 36 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'O' and resid 11 through 14 656 hydrogen bonds defined for protein. 1689 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.32 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 6181 1.35 - 1.49: 5094 1.49 - 1.63: 8070 1.63 - 1.77: 1 1.77 - 1.90: 151 Bond restraints: 19497 Sorted by residual: bond pdb=" CA THR B 71 " pdb=" CB THR B 71 " ideal model delta sigma weight residual 1.528 1.625 -0.097 2.61e-02 1.47e+03 1.38e+01 bond pdb=" C3 MAN P 4 " pdb=" O3 MAN P 4 " ideal model delta sigma weight residual 1.408 1.474 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" CB CYS B 218 " pdb=" SG CYS B 218 " ideal model delta sigma weight residual 1.808 1.903 -0.095 3.30e-02 9.18e+02 8.34e+00 bond pdb=" CG LEU H 33 " pdb=" CD1 LEU H 33 " ideal model delta sigma weight residual 1.521 1.431 0.090 3.30e-02 9.18e+02 7.47e+00 bond pdb=" C3 MAN P 4 " pdb=" C4 MAN P 4 " ideal model delta sigma weight residual 1.524 1.578 -0.054 2.00e-02 2.50e+03 7.17e+00 ... (remaining 19492 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.51: 26227 4.51 - 9.03: 210 9.03 - 13.54: 26 13.54 - 18.06: 3 18.06 - 22.57: 1 Bond angle restraints: 26467 Sorted by residual: angle pdb=" C ASN B 411 " pdb=" N ASP B 412 " pdb=" CA ASP B 412 " ideal model delta sigma weight residual 121.70 137.60 -15.90 1.80e+00 3.09e-01 7.81e+01 angle pdb=" CD1 LEU H 33 " pdb=" CG LEU H 33 " pdb=" CD2 LEU H 33 " ideal model delta sigma weight residual 110.80 94.17 16.63 2.20e+00 2.07e-01 5.71e+01 angle pdb=" CB LEU H 33 " pdb=" CG LEU H 33 " pdb=" CD2 LEU H 33 " ideal model delta sigma weight residual 110.70 88.13 22.57 3.00e+00 1.11e-01 5.66e+01 angle pdb=" C GLY F 597 " pdb=" N CYS F 598 " pdb=" CA CYS F 598 " ideal model delta sigma weight residual 121.54 133.71 -12.17 1.91e+00 2.74e-01 4.06e+01 angle pdb=" C LYS F 601 " pdb=" N LEU F 602 " pdb=" CA LEU F 602 " ideal model delta sigma weight residual 121.54 133.31 -11.77 1.91e+00 2.74e-01 3.80e+01 ... (remaining 26462 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.57: 10973 21.57 - 43.14: 676 43.14 - 64.72: 111 64.72 - 86.29: 52 86.29 - 107.86: 17 Dihedral angle restraints: 11829 sinusoidal: 4843 harmonic: 6986 Sorted by residual: dihedral pdb=" CB CYS B 218 " pdb=" SG CYS B 218 " pdb=" SG CYS B 247 " pdb=" CB CYS B 247 " ideal model delta sinusoidal sigma weight residual 93.00 3.67 89.33 1 1.00e+01 1.00e-02 9.49e+01 dihedral pdb=" CB CYS B 296 " pdb=" SG CYS B 296 " pdb=" SG CYS B 378 " pdb=" CB CYS B 378 " ideal model delta sinusoidal sigma weight residual -86.00 -1.59 -84.41 1 1.00e+01 1.00e-02 8.66e+01 dihedral pdb=" CB CYS B 54 " pdb=" SG CYS B 54 " pdb=" SG CYS B 74 " pdb=" CB CYS B 74 " ideal model delta sinusoidal sigma weight residual 93.00 164.42 -71.42 1 1.00e+01 1.00e-02 6.54e+01 ... (remaining 11826 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 2829 0.113 - 0.226: 190 0.226 - 0.338: 10 0.338 - 0.451: 3 0.451 - 0.564: 1 Chirality restraints: 3033 Sorted by residual: chirality pdb=" CG LEU H 96 " pdb=" CB LEU H 96 " pdb=" CD1 LEU H 96 " pdb=" CD2 LEU H 96 " both_signs ideal model delta sigma weight residual False -2.59 -2.03 -0.56 2.00e-01 2.50e+01 7.95e+00 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.45 0.05 2.00e-02 2.50e+03 7.18e+00 chirality pdb=" C1 BMA d 3 " pdb=" O4 NAG d 2 " pdb=" C2 BMA d 3 " pdb=" O5 BMA d 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 4.95e+00 ... (remaining 3030 not shown) Planarity restraints: 3352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 71 " 0.040 2.00e-02 2.50e+03 5.15e-02 4.64e+01 pdb=" CG PHE H 71 " -0.115 2.00e-02 2.50e+03 pdb=" CD1 PHE H 71 " 0.052 2.00e-02 2.50e+03 pdb=" CD2 PHE H 71 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE H 71 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE H 71 " 0.016 2.00e-02 2.50e+03 pdb=" CZ PHE H 71 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 50 " -0.056 2.00e-02 2.50e+03 4.00e-02 4.00e+01 pdb=" CG TRP I 50 " 0.102 2.00e-02 2.50e+03 pdb=" CD1 TRP I 50 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP I 50 " 0.012 2.00e-02 2.50e+03 pdb=" NE1 TRP I 50 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP I 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP I 50 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 50 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 50 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP I 50 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 29 " -0.028 2.00e-02 2.50e+03 3.33e-02 1.94e+01 pdb=" CG PHE I 29 " 0.077 2.00e-02 2.50e+03 pdb=" CD1 PHE I 29 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE I 29 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 PHE I 29 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE I 29 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE I 29 " 0.002 2.00e-02 2.50e+03 ... (remaining 3349 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4822 2.81 - 3.33: 15815 3.33 - 3.86: 30509 3.86 - 4.38: 33739 4.38 - 4.90: 58764 Nonbonded interactions: 143649 Sorted by model distance: nonbonded pdb=" OG SER B 365 " pdb=" O LYS N 46 " model vdw 2.288 3.040 nonbonded pdb=" OG1 THR K 83 " pdb=" OD1 ASP K 85 " model vdw 2.291 3.040 nonbonded pdb=" O TYR H 49 " pdb=" OG1 THR H 53 " model vdw 2.310 3.040 nonbonded pdb=" O TYR J 49 " pdb=" OG1 THR J 53 " model vdw 2.328 3.040 nonbonded pdb=" OG SER N 79 " pdb=" O LEU N 95 " model vdw 2.335 3.040 ... (remaining 143644 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 58 or resid 68 through 118 or resid 208 through \ 298 or resid 327 through 457 or resid 460 through 503)) selection = (chain 'B' and (resid 33 through 48 or (resid 49 and (name N or name CA or name \ C or name O or name CB )) or resid 50 through 56 or (resid 57 through 58 and (na \ me N or name CA or name C or name O or name CB )) or resid 68 through 86 or (res \ id 87 and (name N or name CA or name C or name O or name CB )) or resid 88 throu \ gh 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or r \ esid 98 through 116 or (resid 117 and (name N or name CA or name C or name O or \ name CB )) or resid 118 or (resid 208 and (name N or name CA or name C or name O \ or name CB )) or resid 209 through 210 or (resid 211 and (name N or name CA or \ name C or name O or name CB )) or resid 212 through 230 or (resid 231 through 23 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 233 through \ 266 or (resid 267 through 269 and (name N or name CA or name C or name O or name \ CB )) or resid 270 through 274 or (resid 275 and (name N or name CA or name C o \ r name O or name CB )) or resid 276 through 357 or (resid 358 and (name N or nam \ e CA or name C or name O or name CB )) or resid 359 through 369 or (resid 370 an \ d (name N or name CA or name C or name O or name CB )) or resid 371 through 380 \ or (resid 381 and (name N or name CA or name C or name O or name CB )) or resid \ 382 through 395 or (resid 396 and (name N or name CA or name C or name O or name \ CB )) or resid 397 or resid 412 through 439 or (resid 440 and (name N or name C \ A or name C or name O or name CB )) or resid 441 through 456 or (resid 457 and ( \ name N or name CA or name C or name O or name CB )) or resid 463 through 464 or \ (resid 465 and (name N or name CA or name C or name O or name CB or name OG1)) o \ r (resid 466 and (name N or name CA or name C or name O or name CB or name CG )) \ or (resid 467 and (name N or name CA or name C or name O or name CB )) or resid \ 468 through 473 or (resid 474 and (name N or name CA or name C or name O or nam \ e CB )) or resid 475 through 501 or (resid 502 and (name N or name CA or name C \ or name O or name CB )) or resid 503)) selection = (chain 'C' and (resid 33 through 58 or resid 68 through 118 or resid 208 through \ 298 or resid 327 through 457 or resid 460 through 503)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = (chain 'F' and (resid 512 through 550 or resid 567 through 664)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 18.590 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 19549 Z= 0.242 Angle : 1.080 22.573 26586 Z= 0.552 Chirality : 0.060 0.564 3033 Planarity : 0.007 0.070 3349 Dihedral : 15.310 107.860 7210 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.97 % Favored : 93.78 % Rotamer: Outliers : 0.15 % Allowed : 0.39 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.03 (0.16), residues: 2379 helix: -2.35 (0.22), residues: 350 sheet: -0.22 (0.19), residues: 753 loop : -1.76 (0.16), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 82B TYR 0.024 0.002 TYR I 90 PHE 0.115 0.003 PHE H 71 TRP 0.102 0.004 TRP I 50 HIS 0.010 0.002 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00503 (19497) covalent geometry : angle 1.06471 (26467) SS BOND : bond 0.01042 ( 37) SS BOND : angle 2.99808 ( 74) hydrogen bonds : bond 0.15595 ( 624) hydrogen bonds : angle 7.41442 ( 1689) link_ALPHA1-3 : bond 0.00644 ( 3) link_ALPHA1-3 : angle 3.59549 ( 9) link_ALPHA1-6 : bond 0.00220 ( 3) link_ALPHA1-6 : angle 1.32495 ( 9) link_BETA1-4 : bond 0.00616 ( 6) link_BETA1-4 : angle 2.63433 ( 18) link_NAG-ASN : bond 0.00359 ( 3) link_NAG-ASN : angle 2.60978 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 504 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ASP cc_start: 0.8107 (t0) cc_final: 0.7681 (t0) REVERT: A 377 ASN cc_start: 0.8524 (p0) cc_final: 0.8282 (p0) REVERT: A 449 ILE cc_start: 0.8523 (mm) cc_final: 0.8212 (mm) REVERT: A 482 GLU cc_start: 0.8687 (mp0) cc_final: 0.8384 (mp0) REVERT: A 486 TYR cc_start: 0.8237 (m-80) cc_final: 0.7721 (m-10) REVERT: B 115 SER cc_start: 0.6614 (t) cc_final: 0.5979 (p) REVERT: B 270 VAL cc_start: 0.8755 (t) cc_final: 0.8535 (p) REVERT: C 85 HIS cc_start: 0.8082 (m170) cc_final: 0.7459 (m170) REVERT: D 543 ASN cc_start: 0.7130 (OUTLIER) cc_final: 0.6831 (t0) REVERT: D 569 THR cc_start: 0.7448 (t) cc_final: 0.7105 (t) REVERT: D 618 ASN cc_start: 0.6598 (p0) cc_final: 0.6081 (p0) REVERT: E 628 TRP cc_start: 0.8240 (m100) cc_final: 0.7543 (t-100) REVERT: F 530 MET cc_start: 0.8578 (tpt) cc_final: 0.8304 (tpt) REVERT: F 539 VAL cc_start: 0.9314 (m) cc_final: 0.9053 (t) REVERT: G 63 PHE cc_start: 0.8794 (m-10) cc_final: 0.8408 (m-10) REVERT: G 90 TYR cc_start: 0.7343 (m-80) cc_final: 0.6909 (m-80) REVERT: G 100 VAL cc_start: 0.8224 (t) cc_final: 0.7852 (t) REVERT: H 24 ARG cc_start: 0.8444 (tpp80) cc_final: 0.8119 (tpp80) REVERT: I 103 TRP cc_start: 0.7509 (m-10) cc_final: 0.6970 (m-10) REVERT: J 3 GLN cc_start: 0.6840 (mm110) cc_final: 0.6584 (tp40) REVERT: J 82 ASP cc_start: 0.6558 (m-30) cc_final: 0.6229 (m-30) REVERT: K 39 GLN cc_start: 0.8471 (tt0) cc_final: 0.8218 (tt0) REVERT: K 95 ASP cc_start: 0.8828 (t0) cc_final: 0.8478 (t0) REVERT: L 11 LEU cc_start: 0.8557 (tp) cc_final: 0.8355 (tp) REVERT: L 49 TYR cc_start: 0.9030 (p90) cc_final: 0.8748 (p90) REVERT: L 71 PHE cc_start: 0.8149 (m-10) cc_final: 0.7896 (m-10) REVERT: L 83 PHE cc_start: 0.7857 (m-80) cc_final: 0.7511 (m-80) REVERT: M 34 ILE cc_start: 0.8269 (mp) cc_final: 0.7691 (mp) REVERT: M 85 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7891 (mm-30) REVERT: N 35 LYS cc_start: 0.8366 (tttp) cc_final: 0.7809 (tptt) REVERT: N 78 ASP cc_start: 0.7380 (p0) cc_final: 0.6945 (p0) REVERT: O 34 ILE cc_start: 0.8724 (mm) cc_final: 0.8266 (mm) outliers start: 3 outliers final: 0 residues processed: 505 average time/residue: 0.1300 time to fit residues: 102.5508 Evaluate side-chains 392 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 391 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 7.9990 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN A 425 ASN C 66 HIS C 374 HIS D 543 ASN D 577 GLN D 590 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 HIS L 70 HIS O 40 GLN O 89 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.180273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.158025 restraints weight = 33870.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.158684 restraints weight = 74852.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.157943 restraints weight = 58283.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.157787 restraints weight = 42835.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.158150 restraints weight = 36545.441| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 19549 Z= 0.186 Angle : 0.685 10.171 26586 Z= 0.350 Chirality : 0.046 0.272 3033 Planarity : 0.005 0.071 3349 Dihedral : 9.109 81.893 2871 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.59 % Favored : 94.16 % Rotamer: Outliers : 0.15 % Allowed : 5.47 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.17), residues: 2379 helix: -1.36 (0.25), residues: 372 sheet: -0.04 (0.19), residues: 717 loop : -1.64 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 617 TYR 0.017 0.002 TYR C 486 PHE 0.052 0.002 PHE H 71 TRP 0.045 0.003 TRP D 571 HIS 0.007 0.001 HIS J 90 Details of bonding type rmsd covalent geometry : bond 0.00429 (19497) covalent geometry : angle 0.67096 (26467) SS BOND : bond 0.00373 ( 37) SS BOND : angle 1.80943 ( 74) hydrogen bonds : bond 0.04509 ( 624) hydrogen bonds : angle 5.80078 ( 1689) link_ALPHA1-3 : bond 0.00327 ( 3) link_ALPHA1-3 : angle 2.96966 ( 9) link_ALPHA1-6 : bond 0.00560 ( 3) link_ALPHA1-6 : angle 2.20506 ( 9) link_BETA1-4 : bond 0.00465 ( 6) link_BETA1-4 : angle 2.89374 ( 18) link_NAG-ASN : bond 0.00531 ( 3) link_NAG-ASN : angle 2.34461 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 468 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ASN cc_start: 0.8432 (OUTLIER) cc_final: 0.8094 (t0) REVERT: A 486 TYR cc_start: 0.8505 (m-80) cc_final: 0.8199 (m-80) REVERT: B 91 GLU cc_start: 0.7896 (pp20) cc_final: 0.7291 (tt0) REVERT: B 103 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7939 (tm-30) REVERT: B 115 SER cc_start: 0.6892 (t) cc_final: 0.6511 (p) REVERT: B 331 CYS cc_start: 0.6173 (m) cc_final: 0.5776 (m) REVERT: C 85 HIS cc_start: 0.8396 (m170) cc_final: 0.7876 (m170) REVERT: C 104 MET cc_start: 0.8703 (ttp) cc_final: 0.8108 (ttp) REVERT: D 618 ASN cc_start: 0.6852 (p0) cc_final: 0.6626 (p0) REVERT: F 530 MET cc_start: 0.9182 (tpt) cc_final: 0.8722 (tpt) REVERT: F 539 VAL cc_start: 0.9372 (m) cc_final: 0.9116 (t) REVERT: F 627 THR cc_start: 0.8707 (p) cc_final: 0.8503 (p) REVERT: F 636 SER cc_start: 0.9033 (p) cc_final: 0.8810 (t) REVERT: G 4 LEU cc_start: 0.8621 (mm) cc_final: 0.8241 (mt) REVERT: G 62 LYS cc_start: 0.7893 (ptmt) cc_final: 0.7427 (ptmm) REVERT: G 63 PHE cc_start: 0.7836 (m-10) cc_final: 0.7386 (m-10) REVERT: H 71 PHE cc_start: 0.5439 (m-10) cc_final: 0.5079 (m-10) REVERT: H 82 ASP cc_start: 0.8095 (p0) cc_final: 0.7658 (p0) REVERT: H 86 TYR cc_start: 0.8109 (m-80) cc_final: 0.7854 (m-10) REVERT: H 91 MET cc_start: 0.5508 (pmm) cc_final: 0.3946 (ptp) REVERT: I 103 TRP cc_start: 0.7000 (m-10) cc_final: 0.6735 (m-10) REVERT: K 95 ASP cc_start: 0.8843 (t0) cc_final: 0.8195 (t0) REVERT: M 34 ILE cc_start: 0.6848 (mp) cc_final: 0.6050 (mp) REVERT: O 34 ILE cc_start: 0.7974 (mm) cc_final: 0.7759 (mm) outliers start: 3 outliers final: 1 residues processed: 471 average time/residue: 0.1291 time to fit residues: 96.7087 Evaluate side-chains 381 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 379 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 61 optimal weight: 0.3980 chunk 193 optimal weight: 0.0870 chunk 78 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 162 optimal weight: 9.9990 chunk 234 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 279 ASN ** D 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN H 89 GLN I 43 GLN I 52 ASN K 100 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.182195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.163944 restraints weight = 33824.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.162482 restraints weight = 73002.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.162849 restraints weight = 63535.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.162341 restraints weight = 47731.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.162587 restraints weight = 49256.416| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19549 Z= 0.131 Angle : 0.630 12.138 26586 Z= 0.318 Chirality : 0.045 0.263 3033 Planarity : 0.004 0.058 3349 Dihedral : 8.666 79.282 2871 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.51 % Favored : 94.28 % Rotamer: Outliers : 0.15 % Allowed : 3.14 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.17), residues: 2379 helix: -0.70 (0.27), residues: 352 sheet: 0.22 (0.20), residues: 733 loop : -1.58 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 82B TYR 0.024 0.001 TYR L 94 PHE 0.042 0.001 PHE H 71 TRP 0.024 0.002 TRP E 571 HIS 0.009 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00301 (19497) covalent geometry : angle 0.61651 (26467) SS BOND : bond 0.00371 ( 37) SS BOND : angle 1.85868 ( 74) hydrogen bonds : bond 0.04013 ( 624) hydrogen bonds : angle 5.50635 ( 1689) link_ALPHA1-3 : bond 0.00432 ( 3) link_ALPHA1-3 : angle 2.49221 ( 9) link_ALPHA1-6 : bond 0.00654 ( 3) link_ALPHA1-6 : angle 1.95074 ( 9) link_BETA1-4 : bond 0.00391 ( 6) link_BETA1-4 : angle 2.31817 ( 18) link_NAG-ASN : bond 0.00334 ( 3) link_NAG-ASN : angle 2.16892 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 479 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 TYR cc_start: 0.8285 (m-80) cc_final: 0.7810 (m-10) REVERT: B 91 GLU cc_start: 0.7779 (pp20) cc_final: 0.7312 (tt0) REVERT: B 102 GLU cc_start: 0.7784 (mp0) cc_final: 0.7355 (tp30) REVERT: B 115 SER cc_start: 0.6946 (t) cc_final: 0.6690 (p) REVERT: B 331 CYS cc_start: 0.5371 (m) cc_final: 0.5099 (m) REVERT: B 338 TRP cc_start: 0.7759 (t-100) cc_final: 0.7490 (t60) REVERT: B 390 LEU cc_start: 0.8499 (mt) cc_final: 0.7121 (mt) REVERT: B 486 TYR cc_start: 0.8910 (m-80) cc_final: 0.8292 (m-10) REVERT: C 85 HIS cc_start: 0.8514 (m170) cc_final: 0.7967 (m170) REVERT: D 543 ASN cc_start: 0.7203 (t0) cc_final: 0.6753 (t0) REVERT: D 588 ARG cc_start: 0.8278 (tpp80) cc_final: 0.8063 (tpp80) REVERT: D 618 ASN cc_start: 0.6790 (p0) cc_final: 0.6390 (p0) REVERT: E 649 SER cc_start: 0.8318 (t) cc_final: 0.8052 (m) REVERT: F 539 VAL cc_start: 0.9415 (m) cc_final: 0.9185 (t) REVERT: G 1 GLN cc_start: 0.7293 (mm110) cc_final: 0.7074 (mm-40) REVERT: G 4 LEU cc_start: 0.8574 (mm) cc_final: 0.8225 (mt) REVERT: G 62 LYS cc_start: 0.7769 (ptmt) cc_final: 0.7323 (ptmm) REVERT: G 63 PHE cc_start: 0.7701 (m-10) cc_final: 0.7342 (m-10) REVERT: H 82 ASP cc_start: 0.7892 (p0) cc_final: 0.7612 (p0) REVERT: H 86 TYR cc_start: 0.8113 (m-80) cc_final: 0.7885 (m-10) REVERT: H 91 MET cc_start: 0.5653 (pmm) cc_final: 0.3877 (ptp) REVERT: I 80 LEU cc_start: 0.6828 (tt) cc_final: 0.6612 (tt) REVERT: K 95 ASP cc_start: 0.8836 (t0) cc_final: 0.8225 (t0) REVERT: M 34 ILE cc_start: 0.6595 (mp) cc_final: 0.5825 (mp) outliers start: 3 outliers final: 2 residues processed: 481 average time/residue: 0.1275 time to fit residues: 97.1250 Evaluate side-chains 377 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 375 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 232 optimal weight: 0.8980 chunk 217 optimal weight: 20.0000 chunk 139 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 149 optimal weight: 0.0470 chunk 20 optimal weight: 8.9990 chunk 136 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 113 optimal weight: 0.2980 chunk 80 optimal weight: 0.9980 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN D 590 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.182381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.164018 restraints weight = 33714.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.163036 restraints weight = 74142.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.163413 restraints weight = 69020.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.163734 restraints weight = 47041.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.163659 restraints weight = 48163.611| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19549 Z= 0.124 Angle : 0.618 12.027 26586 Z= 0.308 Chirality : 0.045 0.249 3033 Planarity : 0.004 0.060 3349 Dihedral : 8.054 73.242 2871 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.59 % Favored : 94.20 % Rotamer: Outliers : 0.10 % Allowed : 3.00 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.17), residues: 2379 helix: -0.42 (0.28), residues: 351 sheet: 0.21 (0.20), residues: 718 loop : -1.46 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 82B TYR 0.015 0.001 TYR J 49 PHE 0.039 0.001 PHE H 71 TRP 0.049 0.002 TRP K 50 HIS 0.006 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00286 (19497) covalent geometry : angle 0.60684 (26467) SS BOND : bond 0.00432 ( 37) SS BOND : angle 1.64078 ( 74) hydrogen bonds : bond 0.03641 ( 624) hydrogen bonds : angle 5.29969 ( 1689) link_ALPHA1-3 : bond 0.00539 ( 3) link_ALPHA1-3 : angle 2.49883 ( 9) link_ALPHA1-6 : bond 0.00731 ( 3) link_ALPHA1-6 : angle 1.93663 ( 9) link_BETA1-4 : bond 0.00377 ( 6) link_BETA1-4 : angle 2.11110 ( 18) link_NAG-ASN : bond 0.00270 ( 3) link_NAG-ASN : angle 1.99506 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 491 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.7175 (p0) cc_final: 0.6404 (p0) REVERT: A 486 TYR cc_start: 0.8260 (m-80) cc_final: 0.7763 (m-10) REVERT: B 91 GLU cc_start: 0.7589 (pp20) cc_final: 0.7252 (tt0) REVERT: B 102 GLU cc_start: 0.7827 (mp0) cc_final: 0.7239 (tp30) REVERT: C 85 HIS cc_start: 0.8536 (m170) cc_final: 0.8012 (m170) REVERT: D 543 ASN cc_start: 0.7166 (t0) cc_final: 0.6710 (t0) REVERT: D 595 ILE cc_start: 0.8205 (tt) cc_final: 0.7935 (tt) REVERT: D 618 ASN cc_start: 0.6583 (p0) cc_final: 0.6229 (p0) REVERT: E 617 ARG cc_start: 0.6962 (mtm-85) cc_final: 0.6733 (mtm-85) REVERT: E 649 SER cc_start: 0.8284 (t) cc_final: 0.7974 (m) REVERT: F 530 MET cc_start: 0.9074 (tpt) cc_final: 0.8510 (tpt) REVERT: F 627 THR cc_start: 0.8803 (p) cc_final: 0.8566 (p) REVERT: G 1 GLN cc_start: 0.7237 (mm110) cc_final: 0.7036 (mm-40) REVERT: G 4 LEU cc_start: 0.8567 (mm) cc_final: 0.8206 (mt) REVERT: G 62 LYS cc_start: 0.7728 (ptmt) cc_final: 0.7271 (ptmm) REVERT: G 63 PHE cc_start: 0.7669 (m-10) cc_final: 0.7352 (m-10) REVERT: H 82 ASP cc_start: 0.7960 (p0) cc_final: 0.7585 (p0) REVERT: H 89 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7696 (pp30) REVERT: H 91 MET cc_start: 0.6069 (pmm) cc_final: 0.3917 (ptp) REVERT: I 103 TRP cc_start: 0.6875 (m-10) cc_final: 0.6554 (m-10) REVERT: K 95 ASP cc_start: 0.8740 (t0) cc_final: 0.8172 (t0) REVERT: M 34 ILE cc_start: 0.6649 (mp) cc_final: 0.5934 (mp) REVERT: O 62 TRP cc_start: 0.8633 (m-10) cc_final: 0.8274 (m-90) outliers start: 2 outliers final: 1 residues processed: 492 average time/residue: 0.1252 time to fit residues: 96.4989 Evaluate side-chains 383 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 381 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 234 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 chunk 151 optimal weight: 0.0470 chunk 228 optimal weight: 0.6980 chunk 205 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 112 optimal weight: 0.0170 chunk 116 optimal weight: 0.5980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** D 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 GLN O 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.183526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.161037 restraints weight = 33655.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.160314 restraints weight = 73289.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.160724 restraints weight = 63629.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.161468 restraints weight = 43400.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.161265 restraints weight = 42349.360| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19549 Z= 0.116 Angle : 0.620 12.124 26586 Z= 0.311 Chirality : 0.045 0.253 3033 Planarity : 0.004 0.070 3349 Dihedral : 7.719 67.919 2871 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.55 % Favored : 94.28 % Rotamer: Outliers : 0.10 % Allowed : 2.23 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.17), residues: 2379 helix: -0.25 (0.29), residues: 350 sheet: 0.29 (0.20), residues: 710 loop : -1.41 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 82B TYR 0.018 0.001 TYR B 486 PHE 0.028 0.001 PHE H 71 TRP 0.034 0.002 TRP K 47 HIS 0.006 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00267 (19497) covalent geometry : angle 0.60838 (26467) SS BOND : bond 0.00362 ( 37) SS BOND : angle 1.79536 ( 74) hydrogen bonds : bond 0.03478 ( 624) hydrogen bonds : angle 5.17498 ( 1689) link_ALPHA1-3 : bond 0.00558 ( 3) link_ALPHA1-3 : angle 2.49320 ( 9) link_ALPHA1-6 : bond 0.00807 ( 3) link_ALPHA1-6 : angle 1.90733 ( 9) link_BETA1-4 : bond 0.00399 ( 6) link_BETA1-4 : angle 1.87679 ( 18) link_NAG-ASN : bond 0.00245 ( 3) link_NAG-ASN : angle 1.97389 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 493 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.7110 (p0) cc_final: 0.6420 (p0) REVERT: A 486 TYR cc_start: 0.8158 (m-80) cc_final: 0.7590 (m-10) REVERT: B 91 GLU cc_start: 0.7566 (pp20) cc_final: 0.7312 (tt0) REVERT: B 102 GLU cc_start: 0.7814 (mp0) cc_final: 0.7320 (tp30) REVERT: B 104 MET cc_start: 0.8340 (tpp) cc_final: 0.8078 (tpp) REVERT: C 82 GLN cc_start: 0.6737 (mm-40) cc_final: 0.6489 (mm-40) REVERT: C 85 HIS cc_start: 0.8433 (m170) cc_final: 0.7745 (m170) REVERT: D 543 ASN cc_start: 0.6932 (t0) cc_final: 0.6651 (t0) REVERT: D 595 ILE cc_start: 0.8127 (tt) cc_final: 0.7789 (tt) REVERT: D 618 ASN cc_start: 0.6416 (p0) cc_final: 0.6110 (p0) REVERT: E 649 SER cc_start: 0.8190 (t) cc_final: 0.7790 (m) REVERT: F 530 MET cc_start: 0.9071 (tpt) cc_final: 0.8618 (tpt) REVERT: G 47 TRP cc_start: 0.8303 (t60) cc_final: 0.7759 (t60) REVERT: G 62 LYS cc_start: 0.7715 (ptmt) cc_final: 0.7188 (ptmm) REVERT: G 63 PHE cc_start: 0.7738 (m-10) cc_final: 0.7428 (m-10) REVERT: H 82 ASP cc_start: 0.7924 (p0) cc_final: 0.7652 (p0) REVERT: H 91 MET cc_start: 0.6003 (pmm) cc_final: 0.3928 (ptp) REVERT: J 70 HIS cc_start: 0.7467 (p-80) cc_final: 0.6891 (t-90) REVERT: J 71 PHE cc_start: 0.6100 (m-80) cc_final: 0.5584 (m-80) REVERT: J 72 THR cc_start: 0.4973 (p) cc_final: 0.4688 (p) REVERT: K 95 ASP cc_start: 0.8665 (t0) cc_final: 0.8071 (t0) REVERT: M 34 ILE cc_start: 0.6847 (mp) cc_final: 0.6105 (mp) REVERT: O 58 ARG cc_start: 0.8040 (mtt180) cc_final: 0.7771 (mtm-85) REVERT: O 62 TRP cc_start: 0.8590 (m-10) cc_final: 0.8258 (m-90) outliers start: 2 outliers final: 1 residues processed: 494 average time/residue: 0.1305 time to fit residues: 101.3305 Evaluate side-chains 384 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 383 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 109 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 231 optimal weight: 10.0000 chunk 146 optimal weight: 8.9990 chunk 167 optimal weight: 9.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN C 99 ASN ** D 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN O 27 HIS O 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.179198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.160659 restraints weight = 33494.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.159021 restraints weight = 74723.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.158590 restraints weight = 63735.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.157411 restraints weight = 52308.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.157698 restraints weight = 44552.098| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 19549 Z= 0.190 Angle : 0.692 12.389 26586 Z= 0.350 Chirality : 0.048 0.490 3033 Planarity : 0.004 0.064 3349 Dihedral : 7.649 63.750 2871 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.73 % Favored : 93.02 % Rotamer: Outliers : 0.10 % Allowed : 2.42 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.17), residues: 2379 helix: -0.38 (0.28), residues: 353 sheet: 0.13 (0.20), residues: 749 loop : -1.47 (0.17), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 82B TYR 0.013 0.002 TYR G 90 PHE 0.025 0.002 PHE H 71 TRP 0.048 0.003 TRP K 50 HIS 0.013 0.002 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00444 (19497) covalent geometry : angle 0.67877 (26467) SS BOND : bond 0.00523 ( 37) SS BOND : angle 1.97562 ( 74) hydrogen bonds : bond 0.04179 ( 624) hydrogen bonds : angle 5.33496 ( 1689) link_ALPHA1-3 : bond 0.00264 ( 3) link_ALPHA1-3 : angle 2.77368 ( 9) link_ALPHA1-6 : bond 0.00722 ( 3) link_ALPHA1-6 : angle 2.08379 ( 9) link_BETA1-4 : bond 0.00495 ( 6) link_BETA1-4 : angle 2.04399 ( 18) link_NAG-ASN : bond 0.00619 ( 3) link_NAG-ASN : angle 2.50934 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 477 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 TYR cc_start: 0.8422 (m-80) cc_final: 0.7968 (m-10) REVERT: B 91 GLU cc_start: 0.7777 (pp20) cc_final: 0.7448 (tt0) REVERT: B 102 GLU cc_start: 0.7892 (mp0) cc_final: 0.7427 (tp30) REVERT: B 104 MET cc_start: 0.8551 (ttm) cc_final: 0.8138 (ttt) REVERT: C 78 ASP cc_start: 0.7143 (t0) cc_final: 0.6792 (t0) REVERT: C 85 HIS cc_start: 0.8622 (m170) cc_final: 0.8199 (m170) REVERT: D 595 ILE cc_start: 0.8241 (tt) cc_final: 0.7987 (tt) REVERT: D 617 ARG cc_start: 0.7899 (mtt180) cc_final: 0.6970 (mtt180) REVERT: D 618 ASN cc_start: 0.6411 (p0) cc_final: 0.6031 (p0) REVERT: G 4 LEU cc_start: 0.8577 (mm) cc_final: 0.8139 (mt) REVERT: G 62 LYS cc_start: 0.7937 (ptmt) cc_final: 0.7402 (ptmm) REVERT: G 63 PHE cc_start: 0.7890 (m-10) cc_final: 0.7602 (m-10) REVERT: H 32 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6470 (mt-10) REVERT: H 82 ASP cc_start: 0.8046 (p0) cc_final: 0.7645 (p0) REVERT: H 91 MET cc_start: 0.6466 (pmm) cc_final: 0.4415 (ptp) REVERT: I 103 TRP cc_start: 0.7031 (m-10) cc_final: 0.6713 (m-10) REVERT: J 49 TYR cc_start: 0.6697 (p90) cc_final: 0.6217 (p90) REVERT: J 53 THR cc_start: 0.7270 (p) cc_final: 0.6879 (p) REVERT: J 70 HIS cc_start: 0.7616 (p-80) cc_final: 0.6987 (t-90) REVERT: K 95 ASP cc_start: 0.8901 (t0) cc_final: 0.8254 (t0) REVERT: L 71 PHE cc_start: 0.7789 (m-10) cc_final: 0.7251 (m-10) REVERT: M 34 ILE cc_start: 0.6980 (mp) cc_final: 0.6388 (mp) REVERT: N 43 PHE cc_start: 0.7258 (m-80) cc_final: 0.6532 (m-10) REVERT: O 26 PHE cc_start: 0.7066 (p90) cc_final: 0.6789 (p90) REVERT: O 58 ARG cc_start: 0.8256 (mtt180) cc_final: 0.7917 (mtm-85) REVERT: O 62 TRP cc_start: 0.8754 (m-10) cc_final: 0.8494 (m-90) outliers start: 2 outliers final: 1 residues processed: 479 average time/residue: 0.1211 time to fit residues: 92.1178 Evaluate side-chains 353 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 352 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 65 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 61 optimal weight: 0.0170 chunk 58 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 186 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 193 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 overall best weight: 1.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN B 295 ASN C 33 ASN ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN ** D 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN H 31 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 GLN O 89 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.178261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.160120 restraints weight = 33777.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.159502 restraints weight = 71123.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.158207 restraints weight = 54469.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.156885 restraints weight = 59381.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.157119 restraints weight = 47173.983| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 19549 Z= 0.184 Angle : 0.691 12.336 26586 Z= 0.349 Chirality : 0.047 0.273 3033 Planarity : 0.004 0.066 3349 Dihedral : 7.501 58.741 2871 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.52 % Favored : 93.23 % Rotamer: Outliers : 0.10 % Allowed : 1.60 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.17), residues: 2379 helix: -0.18 (0.29), residues: 340 sheet: 0.00 (0.19), residues: 764 loop : -1.44 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 82B TYR 0.023 0.002 TYR B 486 PHE 0.019 0.002 PHE H 71 TRP 0.045 0.002 TRP K 50 HIS 0.008 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00432 (19497) covalent geometry : angle 0.67867 (26467) SS BOND : bond 0.00416 ( 37) SS BOND : angle 1.86362 ( 74) hydrogen bonds : bond 0.04075 ( 624) hydrogen bonds : angle 5.35974 ( 1689) link_ALPHA1-3 : bond 0.00420 ( 3) link_ALPHA1-3 : angle 2.65904 ( 9) link_ALPHA1-6 : bond 0.00845 ( 3) link_ALPHA1-6 : angle 1.89352 ( 9) link_BETA1-4 : bond 0.00508 ( 6) link_BETA1-4 : angle 2.32071 ( 18) link_NAG-ASN : bond 0.00647 ( 3) link_NAG-ASN : angle 2.48296 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 456 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.6584 (pm20) cc_final: 0.6286 (pm20) REVERT: A 486 TYR cc_start: 0.8374 (m-80) cc_final: 0.7927 (m-10) REVERT: B 91 GLU cc_start: 0.7771 (pp20) cc_final: 0.7532 (tt0) REVERT: B 102 GLU cc_start: 0.7999 (mp0) cc_final: 0.7474 (tp30) REVERT: B 104 MET cc_start: 0.8599 (ttm) cc_final: 0.8053 (ttt) REVERT: B 338 TRP cc_start: 0.7898 (t-100) cc_final: 0.7677 (t60) REVERT: B 486 TYR cc_start: 0.8560 (m-10) cc_final: 0.8165 (m-10) REVERT: C 78 ASP cc_start: 0.7208 (t0) cc_final: 0.6906 (t0) REVERT: C 85 HIS cc_start: 0.8554 (m170) cc_final: 0.8167 (m170) REVERT: D 595 ILE cc_start: 0.8372 (tt) cc_final: 0.8091 (tt) REVERT: D 617 ARG cc_start: 0.7950 (mtt180) cc_final: 0.7636 (ttt180) REVERT: G 4 LEU cc_start: 0.8586 (mm) cc_final: 0.8163 (mt) REVERT: G 62 LYS cc_start: 0.7952 (ptmt) cc_final: 0.7418 (ptmm) REVERT: G 63 PHE cc_start: 0.7965 (m-10) cc_final: 0.7696 (m-10) REVERT: H 82 ASP cc_start: 0.8011 (p0) cc_final: 0.7707 (p0) REVERT: H 91 MET cc_start: 0.6552 (pmm) cc_final: 0.4884 (ptp) REVERT: I 103 TRP cc_start: 0.7049 (m-10) cc_final: 0.6770 (m-10) REVERT: J 49 TYR cc_start: 0.6805 (p90) cc_final: 0.6270 (p90) REVERT: J 53 THR cc_start: 0.7130 (p) cc_final: 0.6760 (p) REVERT: J 70 HIS cc_start: 0.7620 (p-80) cc_final: 0.6956 (t-90) REVERT: K 95 ASP cc_start: 0.9032 (t0) cc_final: 0.8441 (t0) REVERT: L 71 PHE cc_start: 0.7868 (m-10) cc_final: 0.7297 (m-10) REVERT: O 26 PHE cc_start: 0.6891 (p90) cc_final: 0.6665 (p90) REVERT: O 58 ARG cc_start: 0.8307 (mtt180) cc_final: 0.8035 (mtm-85) REVERT: O 62 TRP cc_start: 0.8751 (m-10) cc_final: 0.8490 (m-90) outliers start: 2 outliers final: 1 residues processed: 457 average time/residue: 0.1187 time to fit residues: 86.0306 Evaluate side-chains 355 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 354 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 63 optimal weight: 0.9980 chunk 153 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 158 optimal weight: 30.0000 chunk 101 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN D 540 GLN D 543 ASN ** D 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 GLN ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.182161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.144053 restraints weight = 33793.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.146929 restraints weight = 64778.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.148249 restraints weight = 43736.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.148547 restraints weight = 30474.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.151508 restraints weight = 24736.006| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 19549 Z= 0.235 Angle : 0.751 12.354 26586 Z= 0.383 Chirality : 0.049 0.266 3033 Planarity : 0.005 0.068 3349 Dihedral : 7.234 59.626 2871 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.78 % Favored : 91.97 % Rotamer: Outliers : 0.05 % Allowed : 1.69 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.17), residues: 2379 helix: -0.50 (0.28), residues: 348 sheet: -0.17 (0.19), residues: 772 loop : -1.52 (0.17), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 94 TYR 0.021 0.002 TYR F 638 PHE 0.023 0.002 PHE J 98 TRP 0.094 0.003 TRP K 50 HIS 0.008 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00550 (19497) covalent geometry : angle 0.73798 (26467) SS BOND : bond 0.00487 ( 37) SS BOND : angle 2.08680 ( 74) hydrogen bonds : bond 0.04604 ( 624) hydrogen bonds : angle 5.51646 ( 1689) link_ALPHA1-3 : bond 0.00584 ( 3) link_ALPHA1-3 : angle 2.96698 ( 9) link_ALPHA1-6 : bond 0.00997 ( 3) link_ALPHA1-6 : angle 1.57003 ( 9) link_BETA1-4 : bond 0.00499 ( 6) link_BETA1-4 : angle 2.32471 ( 18) link_NAG-ASN : bond 0.00693 ( 3) link_NAG-ASN : angle 2.68574 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 448 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.6854 (pm20) cc_final: 0.6626 (pm20) REVERT: A 107 ASP cc_start: 0.6935 (p0) cc_final: 0.5999 (p0) REVERT: A 435 TYR cc_start: 0.6430 (t80) cc_final: 0.6152 (t80) REVERT: A 486 TYR cc_start: 0.8609 (m-80) cc_final: 0.8163 (m-10) REVERT: B 102 GLU cc_start: 0.8061 (mp0) cc_final: 0.7457 (tp30) REVERT: B 104 MET cc_start: 0.8676 (ttm) cc_final: 0.8155 (ttt) REVERT: B 331 CYS cc_start: 0.7007 (m) cc_final: 0.6706 (m) REVERT: B 338 TRP cc_start: 0.8520 (t-100) cc_final: 0.8139 (t60) REVERT: B 486 TYR cc_start: 0.8853 (m-10) cc_final: 0.8398 (m-10) REVERT: C 78 ASP cc_start: 0.7384 (t0) cc_final: 0.6883 (t0) REVERT: C 85 HIS cc_start: 0.8456 (m170) cc_final: 0.8127 (m170) REVERT: D 618 ASN cc_start: 0.5977 (p0) cc_final: 0.5678 (p0) REVERT: F 647 GLU cc_start: 0.9122 (tp30) cc_final: 0.8814 (tp30) REVERT: G 4 LEU cc_start: 0.8742 (mm) cc_final: 0.8416 (mt) REVERT: G 62 LYS cc_start: 0.8422 (ptmt) cc_final: 0.7849 (ptmm) REVERT: G 63 PHE cc_start: 0.8558 (m-10) cc_final: 0.8061 (m-10) REVERT: G 73 LYS cc_start: 0.7866 (mtmt) cc_final: 0.7148 (mttt) REVERT: H 11 LEU cc_start: 0.8159 (tt) cc_final: 0.7957 (tt) REVERT: H 91 MET cc_start: 0.6468 (pmm) cc_final: 0.5074 (ptp) REVERT: I 61 GLN cc_start: 0.6760 (mp10) cc_final: 0.6361 (pp30) REVERT: J 49 TYR cc_start: 0.6796 (p90) cc_final: 0.6481 (p90) REVERT: J 53 THR cc_start: 0.7600 (p) cc_final: 0.7173 (p) REVERT: J 70 HIS cc_start: 0.8355 (p-80) cc_final: 0.7316 (t-90) REVERT: K 39 GLN cc_start: 0.8424 (tt0) cc_final: 0.8020 (tt0) REVERT: L 71 PHE cc_start: 0.8148 (m-10) cc_final: 0.7639 (m-10) REVERT: O 34 ILE cc_start: 0.8306 (mm) cc_final: 0.8084 (mm) outliers start: 1 outliers final: 1 residues processed: 449 average time/residue: 0.1188 time to fit residues: 85.7890 Evaluate side-chains 345 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 344 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 20 optimal weight: 0.1980 chunk 133 optimal weight: 3.9990 chunk 155 optimal weight: 0.0970 chunk 149 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 105 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 223 optimal weight: 0.8980 chunk 50 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 279 ASN B 246 GLN ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN ** D 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 31 ASN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.187391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.147492 restraints weight = 33632.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.149596 restraints weight = 54258.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.150808 restraints weight = 43142.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.151835 restraints weight = 27680.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.153675 restraints weight = 23536.341| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19549 Z= 0.121 Angle : 0.670 12.045 26586 Z= 0.337 Chirality : 0.046 0.252 3033 Planarity : 0.004 0.063 3349 Dihedral : 6.546 59.819 2871 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.63 % Favored : 94.12 % Rotamer: Outliers : 0.05 % Allowed : 0.73 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.17), residues: 2379 helix: -0.41 (0.28), residues: 352 sheet: 0.02 (0.20), residues: 739 loop : -1.47 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG I 82B TYR 0.016 0.002 TYR G 90 PHE 0.013 0.001 PHE H 71 TRP 0.064 0.002 TRP K 50 HIS 0.006 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00279 (19497) covalent geometry : angle 0.65888 (26467) SS BOND : bond 0.00449 ( 37) SS BOND : angle 1.96642 ( 74) hydrogen bonds : bond 0.03510 ( 624) hydrogen bonds : angle 5.23292 ( 1689) link_ALPHA1-3 : bond 0.00632 ( 3) link_ALPHA1-3 : angle 2.38256 ( 9) link_ALPHA1-6 : bond 0.01057 ( 3) link_ALPHA1-6 : angle 1.79421 ( 9) link_BETA1-4 : bond 0.00503 ( 6) link_BETA1-4 : angle 1.64424 ( 18) link_NAG-ASN : bond 0.00308 ( 3) link_NAG-ASN : angle 2.06446 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 465 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.6909 (pm20) cc_final: 0.6673 (pm20) REVERT: A 104 MET cc_start: 0.7144 (mmt) cc_final: 0.6930 (mmm) REVERT: A 435 TYR cc_start: 0.6479 (t80) cc_final: 0.6054 (t80) REVERT: A 486 TYR cc_start: 0.8369 (m-80) cc_final: 0.7743 (m-10) REVERT: B 102 GLU cc_start: 0.8049 (mp0) cc_final: 0.7321 (tp30) REVERT: B 104 MET cc_start: 0.8423 (ttm) cc_final: 0.8044 (ttt) REVERT: B 331 CYS cc_start: 0.6886 (m) cc_final: 0.6568 (m) REVERT: B 338 TRP cc_start: 0.8555 (t-100) cc_final: 0.7900 (t60) REVERT: B 390 LEU cc_start: 0.8798 (mt) cc_final: 0.7490 (mt) REVERT: B 486 TYR cc_start: 0.8542 (m-10) cc_final: 0.8018 (m-10) REVERT: C 78 ASP cc_start: 0.7250 (t0) cc_final: 0.6926 (t0) REVERT: C 85 HIS cc_start: 0.8197 (m170) cc_final: 0.7816 (m170) REVERT: D 588 ARG cc_start: 0.8832 (tpp80) cc_final: 0.8412 (tpp80) REVERT: D 595 ILE cc_start: 0.8400 (tt) cc_final: 0.8047 (tt) REVERT: D 617 ARG cc_start: 0.7886 (mtt180) cc_final: 0.5641 (mpt180) REVERT: D 643 TYR cc_start: 0.7988 (m-10) cc_final: 0.7768 (m-10) REVERT: E 530 MET cc_start: 0.7448 (ppp) cc_final: 0.7154 (ppp) REVERT: F 647 GLU cc_start: 0.9040 (tp30) cc_final: 0.8682 (tp30) REVERT: G 4 LEU cc_start: 0.8631 (mm) cc_final: 0.8305 (mt) REVERT: G 47 TRP cc_start: 0.8529 (t60) cc_final: 0.7613 (t60) REVERT: G 62 LYS cc_start: 0.8373 (ptmt) cc_final: 0.7795 (ptmm) REVERT: G 63 PHE cc_start: 0.8528 (m-10) cc_final: 0.8004 (m-10) REVERT: H 23 CYS cc_start: 0.4264 (t) cc_final: 0.2540 (t) REVERT: I 82 ARG cc_start: 0.6794 (mtm110) cc_final: 0.6513 (mmp-170) REVERT: J 49 TYR cc_start: 0.6703 (p90) cc_final: 0.6372 (p90) REVERT: J 53 THR cc_start: 0.7589 (p) cc_final: 0.7150 (p) REVERT: J 70 HIS cc_start: 0.8367 (p-80) cc_final: 0.7470 (t-90) REVERT: K 47 TRP cc_start: 0.7596 (t60) cc_final: 0.6964 (t60) REVERT: K 74 SER cc_start: 0.8837 (p) cc_final: 0.8584 (t) REVERT: K 75 ILE cc_start: 0.8260 (pt) cc_final: 0.7936 (pt) REVERT: K 95 ASP cc_start: 0.8788 (t0) cc_final: 0.8326 (t0) REVERT: L 71 PHE cc_start: 0.8212 (m-80) cc_final: 0.7736 (m-10) REVERT: M 28 TRP cc_start: 0.3660 (m100) cc_final: 0.3391 (m100) REVERT: O 4 VAL cc_start: 0.7443 (t) cc_final: 0.7171 (p) REVERT: O 34 ILE cc_start: 0.8295 (mm) cc_final: 0.8079 (mm) outliers start: 1 outliers final: 1 residues processed: 466 average time/residue: 0.1165 time to fit residues: 87.4707 Evaluate side-chains 369 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 368 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 91 optimal weight: 3.9990 chunk 226 optimal weight: 20.0000 chunk 202 optimal weight: 2.9990 chunk 103 optimal weight: 0.3980 chunk 133 optimal weight: 5.9990 chunk 211 optimal weight: 0.0030 chunk 84 optimal weight: 0.5980 chunk 169 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 150 optimal weight: 0.1980 chunk 46 optimal weight: 1.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN D 543 ASN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.192354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.157983 restraints weight = 33924.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.157582 restraints weight = 59198.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.159565 restraints weight = 50112.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.159995 restraints weight = 32979.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.162128 restraints weight = 28460.235| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19549 Z= 0.125 Angle : 0.670 11.928 26586 Z= 0.337 Chirality : 0.046 0.324 3033 Planarity : 0.004 0.062 3349 Dihedral : 6.270 59.743 2871 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.05 % Favored : 93.69 % Rotamer: Outliers : 0.05 % Allowed : 0.39 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.17), residues: 2379 helix: -0.37 (0.28), residues: 352 sheet: 0.02 (0.20), residues: 738 loop : -1.44 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 82B TYR 0.014 0.001 TYR L 49 PHE 0.013 0.001 PHE C 468 TRP 0.049 0.002 TRP K 50 HIS 0.011 0.001 HIS K 35 Details of bonding type rmsd covalent geometry : bond 0.00288 (19497) covalent geometry : angle 0.66008 (26467) SS BOND : bond 0.00412 ( 37) SS BOND : angle 1.85352 ( 74) hydrogen bonds : bond 0.03414 ( 624) hydrogen bonds : angle 5.11155 ( 1689) link_ALPHA1-3 : bond 0.00559 ( 3) link_ALPHA1-3 : angle 2.41250 ( 9) link_ALPHA1-6 : bond 0.01025 ( 3) link_ALPHA1-6 : angle 1.55782 ( 9) link_BETA1-4 : bond 0.00501 ( 6) link_BETA1-4 : angle 1.60207 ( 18) link_NAG-ASN : bond 0.00262 ( 3) link_NAG-ASN : angle 2.06939 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 459 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.6822 (pm20) cc_final: 0.6561 (pm20) REVERT: A 104 MET cc_start: 0.6675 (mmt) cc_final: 0.5861 (mmt) REVERT: A 107 ASP cc_start: 0.6524 (p0) cc_final: 0.5586 (p0) REVERT: A 435 TYR cc_start: 0.6209 (t80) cc_final: 0.5793 (t80) REVERT: A 486 TYR cc_start: 0.8371 (m-80) cc_final: 0.7787 (m-10) REVERT: B 102 GLU cc_start: 0.7957 (mp0) cc_final: 0.7496 (tp30) REVERT: B 104 MET cc_start: 0.8321 (ttm) cc_final: 0.7871 (ttt) REVERT: B 338 TRP cc_start: 0.8345 (t-100) cc_final: 0.7963 (t60) REVERT: B 486 TYR cc_start: 0.8573 (m-10) cc_final: 0.7984 (m-10) REVERT: C 78 ASP cc_start: 0.7166 (t0) cc_final: 0.6908 (t0) REVERT: C 85 HIS cc_start: 0.8153 (m170) cc_final: 0.7691 (m170) REVERT: D 595 ILE cc_start: 0.8373 (tt) cc_final: 0.7972 (tt) REVERT: D 617 ARG cc_start: 0.7804 (mtt180) cc_final: 0.6481 (mmt90) REVERT: D 643 TYR cc_start: 0.8042 (m-10) cc_final: 0.7823 (m-10) REVERT: E 530 MET cc_start: 0.7252 (ppp) cc_final: 0.6962 (ppp) REVERT: G 4 LEU cc_start: 0.8535 (mm) cc_final: 0.7953 (mt) REVERT: G 47 TRP cc_start: 0.8437 (t60) cc_final: 0.7690 (t60) REVERT: G 62 LYS cc_start: 0.8194 (ptmt) cc_final: 0.7584 (ptmm) REVERT: G 63 PHE cc_start: 0.8239 (m-10) cc_final: 0.7903 (m-10) REVERT: G 73 LYS cc_start: 0.7731 (mtmt) cc_final: 0.6978 (mttt) REVERT: H 23 CYS cc_start: 0.3701 (t) cc_final: 0.2342 (t) REVERT: H 86 TYR cc_start: 0.8306 (m-80) cc_final: 0.8096 (m-10) REVERT: J 49 TYR cc_start: 0.6484 (p90) cc_final: 0.6152 (p90) REVERT: J 53 THR cc_start: 0.7308 (p) cc_final: 0.6855 (p) REVERT: J 70 HIS cc_start: 0.7977 (p-80) cc_final: 0.7302 (t-90) REVERT: K 74 SER cc_start: 0.8759 (p) cc_final: 0.8416 (t) REVERT: K 75 ILE cc_start: 0.8177 (pt) cc_final: 0.7863 (pt) REVERT: K 95 ASP cc_start: 0.8643 (t0) cc_final: 0.8126 (t0) REVERT: L 71 PHE cc_start: 0.8043 (m-80) cc_final: 0.7475 (m-10) outliers start: 1 outliers final: 1 residues processed: 460 average time/residue: 0.1151 time to fit residues: 86.2092 Evaluate side-chains 362 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 361 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 190 optimal weight: 3.9990 chunk 10 optimal weight: 30.0000 chunk 117 optimal weight: 5.9990 chunk 213 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 71 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 217 optimal weight: 30.0000 chunk 198 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 HIS D 543 ASN D 577 GLN D 591 GLN D 616 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 550 GLN H 90 HIS ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 30 ASN O 40 GLN O 89 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.181716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.148808 restraints weight = 33948.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.153410 restraints weight = 71074.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.152791 restraints weight = 30191.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.153352 restraints weight = 25783.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.153816 restraints weight = 21355.804| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.106 19549 Z= 0.351 Angle : 0.903 10.531 26586 Z= 0.466 Chirality : 0.053 0.285 3033 Planarity : 0.006 0.069 3349 Dihedral : 7.141 59.699 2871 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.74 % Favored : 90.96 % Rotamer: Outliers : 0.10 % Allowed : 0.77 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.17), residues: 2379 helix: -1.22 (0.26), residues: 357 sheet: -0.29 (0.19), residues: 773 loop : -1.74 (0.17), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 617 TYR 0.025 0.003 TYR G 97 PHE 0.028 0.003 PHE C 53 TRP 0.113 0.004 TRP K 50 HIS 0.011 0.002 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00821 (19497) covalent geometry : angle 0.88862 (26467) SS BOND : bond 0.00604 ( 37) SS BOND : angle 2.36890 ( 74) hydrogen bonds : bond 0.05684 ( 624) hydrogen bonds : angle 5.92462 ( 1689) link_ALPHA1-3 : bond 0.00401 ( 3) link_ALPHA1-3 : angle 2.87778 ( 9) link_ALPHA1-6 : bond 0.00511 ( 3) link_ALPHA1-6 : angle 1.76371 ( 9) link_BETA1-4 : bond 0.00828 ( 6) link_BETA1-4 : angle 2.86392 ( 18) link_NAG-ASN : bond 0.01066 ( 3) link_NAG-ASN : angle 3.50910 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2820.22 seconds wall clock time: 49 minutes 49.29 seconds (2989.29 seconds total)